The world is in an alternative 19th century, as recorded by man. A second industrial revolution is underway, though hidden away there is magic and even further advanced technology, kept secret from the world. A new age of thought has been ushered in. The Victorian era is well underway.

Unbeknownst to the aristocracy, the middle class, and the poor, among them there is a fourth class: the Church, which does not consist of a horde of stuffy old men, but an entire secret order of men and women, young and old, who fight in the name of God. They call themselves the Black Order, and their warriors, Exorcists. And little does the world know, there is a heated religious war ensuing beneath the layer of all the petty political claims for land.

But who do they fight against? The descendants of Noah himself, come together from wherever the family line has lead them, and with them, there is a strange man calling himself the Millennium Earl, their "employer," who wishes to destroy the world. The Earl also wields various Akuma, which are half-monster, half-machine, formed out of the souls of the dead. But why would the children of Noah fight so vehemently against those who claim to serve God?

Now a strange material called Innocence has been broken by the Earl and spread throughout the universe. It calls others forth, forcing them to take a place in this war. But who will these strange people from other worlds side with? And at what cost, to them or the world?